HEADER HYDROLASE/HYDROLASE INHIBITOR 20-NOV-13 4YIK TITLE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'(3')-DEOXYRIBONUCLEOTIDASE IN TITLE 2 COMPLEX WITH THE INHIBITOR PB-PVU COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-227; COMPND 5 SYNONYM: 5',3'-NUCLEOTIDASE,MITOCHONDRIAL,DEOXY-5'-NUCLEOTIDASE 2, COMPND 6 DNT-2; COMPND 7 EC: 3.1.3.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NT5M, DNT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 5'-NUCLEOTIDASE, DEPHOSPHORYLATION, PHOSPHORYLATION, HAD-LIKE, KEYWDS 2 MITOCHONDRIA, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,P.REZACOVA,J.BRYNDA REVDAT 4 10-JAN-24 4YIK 1 REMARK REVDAT 3 06-FEB-19 4YIK 1 JRNL REVDAT 2 06-SEP-17 4YIK 1 LINK SITE ATOM REVDAT 1 09-SEP-15 4YIK 0 JRNL AUTH P.PACHL,O.SIMAK,P.REZACOVA,M.FABRY,M.BUDESINSKY,I.ROSENBERG, JRNL AUTH 2 J.BRYNDA JRNL TITL STRUCTURE-BASED DESIGN OF A BISPHOSPHONATE JRNL TITL 2 5'(3')-DEOXYRIBONUCLEOTIDASE INHIBITOR JRNL REF MEDCHEMCOMM V. 6 1635 2015 JRNL REFN ISSN 2040-2503 JRNL DOI 10.1039/C5MD00235D REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 49321 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2497 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3425 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1636 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : 0.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.001 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1818 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1721 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2462 ; 1.935 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3948 ; 0.885 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 213 ; 6.155 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;26.691 ;22.824 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 297 ;12.117 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.707 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 251 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1980 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 426 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 824 ; 1.539 ; 1.628 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 825 ; 1.538 ; 1.627 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1033 ; 2.377 ; 2.432 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): -3.9766 31.7574 22.7743 REMARK 3 T TENSOR REMARK 3 T11: 0.0344 T22: 0.0259 REMARK 3 T33: 0.0293 T12: -0.0125 REMARK 3 T13: 0.0218 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.5141 L22: 0.4904 REMARK 3 L33: 0.1672 L12: -0.1767 REMARK 3 L13: -0.2008 L23: 0.0244 REMARK 3 S TENSOR REMARK 3 S11: 0.0511 S12: -0.0271 S13: 0.0934 REMARK 3 S21: -0.0632 S22: -0.0114 S23: -0.0758 REMARK 3 S31: -0.0586 S32: 0.0313 S33: -0.0397 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 107 A 204 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5554 15.5873 19.3032 REMARK 3 T TENSOR REMARK 3 T11: 0.0151 T22: 0.0275 REMARK 3 T33: 0.0190 T12: 0.0012 REMARK 3 T13: 0.0102 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.4209 L22: 0.1621 REMARK 3 L33: 0.1991 L12: 0.1119 REMARK 3 L13: -0.1749 L23: -0.0318 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: 0.0047 S13: -0.0439 REMARK 3 S21: -0.0116 S22: -0.0130 S23: -0.0443 REMARK 3 S31: -0.0177 S32: -0.0024 S33: 0.0000 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 205 A 227 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3199 11.9650 11.5474 REMARK 3 T TENSOR REMARK 3 T11: 0.0340 T22: 0.0622 REMARK 3 T33: 0.0590 T12: -0.0117 REMARK 3 T13: 0.0437 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 0.3551 L22: 0.7517 REMARK 3 L33: 1.3732 L12: 0.0555 REMARK 3 L13: 0.1925 L23: 0.0977 REMARK 3 S TENSOR REMARK 3 S11: -0.0773 S12: 0.0943 S13: -0.0979 REMARK 3 S21: -0.0911 S22: 0.0819 S23: -0.1412 REMARK 3 S31: -0.0283 S32: 0.1596 S33: -0.0046 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 306 A 306 REMARK 3 ORIGIN FOR THE GROUP (A): -3.6496 24.7256 28.1179 REMARK 3 T TENSOR REMARK 3 T11: 0.0192 T22: 0.0357 REMARK 3 T33: 0.0229 T12: 0.0067 REMARK 3 T13: 0.0014 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.2926 L22: 1.7717 REMARK 3 L33: 4.1313 L12: 0.1463 REMARK 3 L13: -1.9241 L23: 1.2735 REMARK 3 S TENSOR REMARK 3 S11: 0.0303 S12: 0.0331 S13: -0.0659 REMARK 3 S21: 0.0703 S22: -0.0085 S23: -0.1455 REMARK 3 S31: 0.0076 S32: -0.0575 S33: -0.0218 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4YIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.915 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49438 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.483 REMARK 200 RESOLUTION RANGE LOW (A) : 60.641 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.74500 REMARK 200 R SYM FOR SHELL (I) : 0.74500 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 4L6A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 8% PEG8000, 10% GYCEROL, PH 4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.09500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.93500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.93500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.64250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.93500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.93500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.54750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.93500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.93500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.64250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.93500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.93500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.54750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.09500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.09500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 607 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 MET A 42 -69.48 -98.41 REMARK 500 VAL A 45 -54.13 -129.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 308 REMARK 610 PEG A 309 REMARK 610 PEG A 310 REMARK 610 PEG A 311 REMARK 610 PEG A 312 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ASP A 43 O 87.2 REMARK 620 3 ASP A 176 OD1 86.7 90.4 REMARK 620 4 2O2 A 306 OBG 101.2 95.7 170.3 REMARK 620 5 HOH A 448 O 89.5 176.6 88.5 85.9 REMARK 620 6 HOH A 465 O 170.2 88.0 84.9 87.8 95.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2O2 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 313 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YIH RELATED DB: PDB REMARK 900 4YIH CONTAINS THE SAME LIGAND DBREF 4YIK A 32 227 UNP Q9NPB1 NT5M_HUMAN 32 227 SEQADV 4YIK SER A 27 UNP Q9NPB1 EXPRESSION TAG SEQADV 4YIK ASN A 28 UNP Q9NPB1 EXPRESSION TAG SEQADV 4YIK ALA A 29 UNP Q9NPB1 EXPRESSION TAG SEQADV 4YIK ALA A 30 UNP Q9NPB1 EXPRESSION TAG SEQADV 4YIK SER A 31 UNP Q9NPB1 EXPRESSION TAG SEQRES 1 A 201 SER ASN ALA ALA SER GLY GLY ARG ALA LEU ARG VAL LEU SEQRES 2 A 201 VAL ASP MET ASP GLY VAL LEU ALA ASP PHE GLU GLY GLY SEQRES 3 A 201 PHE LEU ARG LYS PHE ARG ALA ARG PHE PRO ASP GLN PRO SEQRES 4 A 201 PHE ILE ALA LEU GLU ASP ARG ARG GLY PHE TRP VAL SER SEQRES 5 A 201 GLU GLN TYR GLY ARG LEU ARG PRO GLY LEU SER GLU LYS SEQRES 6 A 201 ALA ILE SER ILE TRP GLU SER LYS ASN PHE PHE PHE GLU SEQRES 7 A 201 LEU GLU PRO LEU PRO GLY ALA VAL GLU ALA VAL LYS GLU SEQRES 8 A 201 MET ALA SER LEU GLN ASN THR ASP VAL PHE ILE CYS THR SEQRES 9 A 201 SER PRO ILE LYS MET PHE LYS TYR CYS PRO TYR GLU LYS SEQRES 10 A 201 TYR ALA TRP VAL GLU LYS TYR PHE GLY PRO ASP PHE LEU SEQRES 11 A 201 GLU GLN ILE VAL LEU THR ARG ASP LYS THR VAL VAL SER SEQRES 12 A 201 ALA ASP LEU LEU ILE ASP ASP ARG PRO ASP ILE THR GLY SEQRES 13 A 201 ALA GLU PRO THR PRO SER TRP GLU HIS VAL LEU PHE THR SEQRES 14 A 201 ALA CYS HIS ASN GLN HIS LEU GLN LEU GLN PRO PRO ARG SEQRES 15 A 201 ARG ARG LEU HIS SER TRP ALA ASP ASP TRP LYS ALA ILE SEQRES 16 A 201 LEU ASP SER LYS ARG PRO HET MG A 301 1 HET GOL A 302 6 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HET 2O2 A 306 33 HET TRS A 307 8 HET PEG A 308 4 HET PEG A 309 4 HET PEG A 310 4 HET PEG A 311 5 HET PEG A 312 4 HET PO4 A 313 5 HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM 2O2 1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D- HETNAM 2 2O2 THREO-PENTOFURANOSYL}-5-[(E)-2- HETNAM 3 2O2 PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 2 MG MG 2+ FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 2O2 C18 H20 N2 O11 P2 FORMUL 8 TRS C4 H12 N O3 1+ FORMUL 9 PEG 5(C4 H10 O3) FORMUL 14 PO4 O4 P 3- FORMUL 15 HOH *263(H2 O) HELIX 1 AA1 ASP A 48 PHE A 61 1 14 HELIX 2 AA2 ALA A 68 ARG A 72 5 5 HELIX 3 AA3 TRP A 76 ARG A 85 1 10 HELIX 4 AA4 GLY A 87 GLU A 97 1 11 HELIX 5 AA5 GLY A 110 LEU A 121 1 12 HELIX 6 AA6 TYR A 138 GLY A 152 1 15 HELIX 7 AA7 PRO A 153 GLU A 157 5 5 HELIX 8 AA8 ASP A 217 SER A 224 1 8 SHEET 1 AA1 6 ILE A 159 LEU A 161 0 SHEET 2 AA1 6 THR A 124 THR A 130 1 N ILE A 128 O VAL A 160 SHEET 3 AA1 6 LEU A 36 VAL A 40 1 N LEU A 36 O ASP A 125 SHEET 4 AA1 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 AA1 6 GLU A 190 PHE A 194 1 O VAL A 192 N LEU A 173 SHEET 6 AA1 6 ARG A 209 LEU A 211 1 O ARG A 209 N LEU A 193 LINK OD2 ASP A 41 MG MG A 301 1555 1555 2.02 LINK O ASP A 43 MG MG A 301 1555 1555 2.08 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.12 LINK MG MG A 301 OBGA2O2 A 306 1555 1555 2.05 LINK MG MG A 301 O HOH A 448 1555 1555 2.08 LINK MG MG A 301 O HOH A 465 1555 1555 2.12 CISPEP 1 PRO A 206 PRO A 207 0 4.75 SITE 1 AC1 6 ASP A 41 ASP A 43 ASP A 176 2O2 A 306 SITE 2 AC1 6 HOH A 465 HOH A 448 SITE 1 AC2 9 SER A 27 ASN A 28 ALA A 119 THR A 124 SITE 2 AC2 9 ASP A 125 VAL A 126 GLN A 158 HOH A 585 SITE 3 AC2 9 HOH A 414 SITE 1 AC3 9 GLY A 110 GLU A 113 ALA A 114 TRP A 214 SITE 2 AC3 9 ALA A 215 ASP A 216 TRP A 218 HOH A 620 SITE 3 AC3 9 HOH A 406 SITE 1 AC4 6 TRP A 76 ARG A 177 PRO A 178 ASP A 179 SITE 2 AC4 6 HOH A 403 HOH A 423 SITE 1 AC5 8 ARG A 37 SER A 169 ALA A 170 ASP A 171 SITE 2 AC5 8 SER A 188 HOH A 440 HOH A 592 HOH A 429 SITE 1 AC6 24 ASP A 41 ASP A 43 PHE A 49 PHE A 75 SITE 2 AC6 24 TRP A 76 VAL A 77 TRP A 96 SER A 131 SITE 3 AC6 24 ILE A 133 LYS A 134 ARG A 163 MG A 301 SITE 4 AC6 24 TRS A 307 HOH A 573 HOH A 465 HOH A 422 SITE 5 AC6 24 HOH A 448 HOH A 410 HOH A 418 HOH A 442 SITE 6 AC6 24 HOH A 480 HOH A 427 HOH A 474 HOH A 438 SITE 1 AC7 6 ASP A 43 PHE A 49 PHE A 102 ILE A 133 SITE 2 AC7 6 2O2 A 306 HOH A 410 SITE 1 AC8 10 ARG A 72 ARG A 73 CYS A 197 HIS A 198 SITE 2 AC8 10 ASN A 199 GLN A 200 HIS A 201 LEU A 202 SITE 3 AC8 10 HOH A 432 HOH A 560 SITE 1 AC9 9 GLU A 148 ARG A 210 HIS A 212 ASP A 216 SITE 2 AC9 9 HOH A 407 HOH A 411 HOH A 446 HOH A 452 SITE 3 AC9 9 HOH A 471 SITE 1 AD1 9 ASN A 28 ALA A 29 GLY A 33 ARG A 34 SITE 2 AD1 9 ALA A 35 ASP A 125 ALA A 183 HOH A 484 SITE 3 AD1 9 HOH A 598 SITE 1 AD2 7 PHE A 103 LYS A 149 PRO A 207 ARG A 208 SITE 2 AD2 7 ARG A 209 HOH A 445 HOH A 529 SITE 1 AD3 6 GLU A 104 LYS A 149 HOH A 428 HOH A 413 SITE 2 AD3 6 HOH A 564 HOH A 420 SITE 1 AD4 7 PRO A 178 ASP A 179 ILE A 180 TRP A 189 SITE 2 AD4 7 HIS A 191 ARG A 208 HOH A 576 CRYST1 73.870 73.870 106.190 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013537 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009417 0.00000